I don't believe that this is possible but I'd like to get confirmation on this assumption either way.

Background

I have ten site collections in a single web application. I have a set of content types that I want to be used on three of these site collections. They contain a number of site columns and I really don't want to muck up the other site collections with irrelivent site columns and content types that may cause more confusion then good to the end user.

Question

Can you target specific site collections with a content type hub?
If not, what are the drawbacks of deploying and updating content types through a feature?

Turns out only web applications subscribe to hubs not site collections. If you want to have two different site collections with subscribe to two different content type hubs, they need to be in two different web applications.

The only way around this is by creating a custom solution and not using the CT Hub at all.